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TAXONOMY—THE VOCABULARY OF MEDICAL MICROBIOLOGY

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One has only to peruse the table of contents of this book to appreciate the diversity of medical pathogens that are associated with infectious diseases. It has been estimated that we currently have the capacity to identify fewer than 10% of the pathogens responsible for causing human disease. This is due to our inability to culture or target these organisms using molecular probes. The diversity of even these identifiable pathogens alone is so great that it is important to appreciate the subtleties associated with each infectious agent. The reason for understanding these differences is significant because each infectious agent has specifically adapted to a particular mode(s) of transmission, a mechanism(s) to grow in a human host (colonization), and a mechanism(s) to cause disease (pathology). As such, a vocabulary that consistently communicates the unique characteristics of infectious organisms to students, microbiologists, and health care workers is critical to avoid the chaos that would ensue without the organizational guidelines of bacterial taxonomy (Gk. taxon = arrangement; eg, the classification of organisms in an ordered system that indicates a natural relationship).

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Identification, classification, and nomenclature are three separate but interrelated areas of bacterial taxonomy. Each area is critical to the ultimate goal of accurately studying the infectious diseases and precisely communicating these to others in the field.

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Identification is practical use of a classification scheme to (1) isolate and distinguish specific organisms among the mix of complex microbial flora, (2) verify the authenticity or special properties of a culture in a clinical setting, and (3) isolate the causative agent of a disease. The latter may lead to the selection of specific pharmacologic treatments directed toward their eradication, a vaccine mitigating their pathology, or a public health measure (eg, handwashing) that prevents further transmission.

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Identification schemes are not classification schemes, although there may be some superficial similarity. For example, the popular literature has reported Escherichia coli as being a cause of hemolytic uremic syndrome (HUS) in infants. There are hundreds of different strains that are classified as E coli but only a few that are associated with HUS. These strains can be “identified” from the many other E coli strains by antibody reactivity with their O-, H-, and K-antigens, as described in Chapter 2 (eg, E coli O157:H7). However, they are more broadly classified as a member of the family Enterobacteriaceae.

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In a microbiologic context, classification is the categorization of organisms into taxonomic groups. Experimental and observational techniques are required for taxonomic classification. This is because biochemical, physiologic, genetic, and morphologic properties are historically necessary for establishing a taxonomic rank. This area of microbiology is necessarily dynamic as the tools continue to evolve (eg, new methods of microscopy, biochemical analysis, and computational nucleic acid biology).

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Nomenclature refers to the naming of an organism by an established group of scientific and medical professionals. This is arguably ...

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